{
"@context": "/terms/",
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"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3364ARLO",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_HTO_LW428"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3364ARLO](/auxiliary-sets/IGVFDS3364ARLO/) has sequence file(s): [IGVFFI8532WKSQ](/sequence-files/IGVFFI8532WKSQ/), [IGVFFI4200FCBP](/sequence-files/IGVFFI4200FCBP/), [IGVFFI2569OGTA](/sequence-files/IGVFFI2569OGTA/), [IGVFFI5449YBBK](/sequence-files/IGVFFI5449YBBK/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS3364ARLO/"
}
]
},
"award": {
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"component": "functional characterization",
"contact_pi": {
"@id": "/users/95d84f03-8ce0-489c-a755-f33ced139c5d/",
"title": "Gary Hon"
},
"title": "Multiscale functional characterization of genomic variation in human developmental disorders"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS0346MQBH/",
"accession": "IGVFDS0346MQBH",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI9879UTKX/",
"accession": "IGVFFI9879UTKX",
"content_type": "guide RNA sequences",
"status": "in progress",
"summary": "guide RNA sequences"
}
],
"status": "preview",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2024-08-16T20:05:08.827809+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "cell hashing barcode sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI8532WKSQ/",
"accession": "IGVFFI8532WKSQ",
"aliases": [
"gary-hon:LW428C_6_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T21:27:40.923679+00:00",
"file_format": "fastq",
"file_size": 511439141,
"href": "/sequence-files/IGVFFI8532WKSQ/@@download/IGVFFI8532WKSQ.fastq.gz",
"md5sum": "ebf9d495715a3614f90906ed71a18b48",
"s3_uri": "s3://igvf-files/2025/01/14/84e21f52-9768-4714-ae98-1fd3b32369a1/IGVFFI8532WKSQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0022841/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/HTO//LW428C_S22_L006_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4200FCBP/",
"accession": "IGVFFI4200FCBP",
"aliases": [
"gary-hon:LW428C_6_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T21:27:53.672203+00:00",
"file_format": "fastq",
"file_size": 486111533,
"href": "/sequence-files/IGVFFI4200FCBP/@@download/IGVFFI4200FCBP.fastq.gz",
"md5sum": "de562253647800a2039df8ef5b4ba5f3",
"s3_uri": "s3://igvf-files/2025/01/14/68f2cc61-3d38-4717-8082-f104c3ad3135/IGVFFI4200FCBP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0022841/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/HTO//LW428C_S22_L006_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2569OGTA/",
"accession": "IGVFFI2569OGTA",
"aliases": [
"gary-hon:LW428C_6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T21:28:06.756953+00:00",
"file_format": "fastq",
"file_size": 4371032724,
"href": "/sequence-files/IGVFFI2569OGTA/@@download/IGVFFI2569OGTA.fastq.gz",
"md5sum": "ff9bbe88d7ceb56170d8185eb21ec4d6",
"s3_uri": "s3://igvf-files/2025/01/14/8d4bb9dd-06bf-4edb-92f7-28e19a94b631/IGVFFI2569OGTA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0022841/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/HTO//LW428C_S22_L006_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5449YBBK/",
"accession": "IGVFFI5449YBBK",
"aliases": [
"gary-hon:LW428C_6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T21:28:51.985417+00:00",
"file_format": "fastq",
"file_size": 4651972358,
"href": "/sequence-files/IGVFFI5449YBBK/@@download/IGVFFI5449YBBK.fastq.gz",
"md5sum": "465d8ea50a089b5f5995e59aff7ebcc1",
"s3_uri": "s3://igvf-files/2025/01/14/ab2318be-4877-4cd8-8fe8-f1c72e1c4b5e/IGVFFI5449YBBK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0022841/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/HTO//LW428C_S22_L006_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5498SDRJ/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS4629NPBV/",
"accession": "IGVFDS4629NPBV",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW428"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9285BBSI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9285BBSI",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW428"
],
"cellular_sub_pool": "subpool_LW428",
"classifications": [
"differentiated cell specimen"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW428) modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2025-01-14T21:27:40.923679+00:00",
"summary": "cell hashing barcode sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "f6206dde-fe05-4eaa-ace7-1a31aa6343f8"
}